Just to add to the importance of hypoxia, many of the "disqualifying" conditions (those for which you may receive a Special Issuance) are exacerbated by hypoxia. Problems like a potential seizure disorder become much worse at altitude (and it does not necessarily have to be 25,000 feet).
When I receive letters to the FAA to review from physicians who know nothing about altitude physiology, it becomes quite clear why there is frequently confusion on the part of the pilot whose doc told them they would be OK to fly. Altutude and the effects of hypoxia are significant.
Here is the link to the FAA's brochure on hypoxia.
http://www.faa.gov/pilots/safety/pil...ia/hypoxia.pdf